SPX-101 is stable in and retains function after exposure to cystic fibrosis sputum

Background: In healthy lungs, epithelial sodium channel (ENaC) is regulated by short, palate, lung, and nasal clone 1 (SPLUNC1). In cystic fibrosis (CF), ENaC is hyperactivated in part due to a loss of SPLUNC1 function. We have developed SPX-101 to replace the lost function of SPLUNC1 in the CF lung. Methods: Expression of SPLUNC1 was determined in sputum from healthy and CF donors. Stability of SPLUNC1, S18 (the ENaC regulatory domain of SPLUNC1), and SPX-101 was determined in sputum from CF donors and towards neutrophil elastase. Activity of SPX-101 after exposure to CF sputum was determined in airway epithelial cells from CF donors and in the βENaC transgenic mouse model. Results: SPLUNC1 protein expression is significantly reduced in CF as compared to healthy sputum. SPLUNC1 is rapidly degraded in CF sputum as well as by a number of individual proteases known to be found in the sputum. SPX-101, but not S18, is stable in CF sputum. Finally, SPX-101 retains its ability to internalize ENaC, regulate airway surface liquid height, and increase survival of βENaC mice after exposure to CF sputum. Conclusions: Our results demonstrate that SPX-101, but not SPLUNC1 or S18, is stable in CF sputum. These results support the therapeutic development of SPX-101 for the treatment of cystic fibrosis.Fil: Sesma, Juliana. Spyryx Biosciences; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Wu, Bryant. Spyryx Biosciences; Estados UnidosFil: Stuhlmiller, Timothy J.. Spyryx Biosciences; Estados UnidosFil: Scott, David W.. Spyryx Biosciences; Estados Unido

Tracing organic matter composition and distribution and its role on arsenic release in shallow Cambodian groundwaters

Biogeochemical processes that utilize dissolved organic carbon are widely thought to be responsible for the liberation of arsenic from sediments to shallow groundwater in south and southeast Asia. The accumulation of this known carcinogen to hazardously high concentrations has occurred in the primary source of drinking water in large parts of densely populated countries in this region. Both surface and sedimentary sources of organic matter have been suggested to contribute dissolved organic carbon in these aquifers. However, identification of the source of organic carbon responsible for driving arsenic release remains enigmatic and even controversial. Here, we provide the most extensive interrogation to date of the isotopic signature of ground and surface waters at a known arsenic hotspot in Cambodia. We present tritium and radiocarbon data that demonstrates that recharge through ponds and/or clay windows can transport young, surface derived organic matter in to groundwater to depths of 44 m under natural flow conditions. Young organic matter dominates the dissolved organic carbon pool in groundwater that is in close proximity to these surface water sources and we suggest this is likely a regional relationship. In locations distal to surface water contact, dissolved organic carbon represents a mixture of both young surface and older sedimentary derived organic matter. Ground-surface water interaction therefore strongly influences the average dissolved organic carbon age and how this is distributed spatially across the field site. Arsenic mobilization rates appear to be controlled by the age of dissolved organic matter present in these groundwaters. Arsenic concentrations in shallow groundwaters (< 20 m) increase by 1 μg/l for every year increase in dissolved organic carbon age compared to only 0.25 μg/l for every year increase in dissolved organic carbon age in deeper (> 20 m) groundwaters. We suggest that, while the rate of arsenic release is greatest in shallow aquifer sediments, arsenic release also occurs in deeper aquifer sediments and as such remains an important process in controlling the spatial distribution of arsenic in the groundwaters of SE Asia. Our findings suggest that any anthropogenic activities that alter the source of groundwater recharge or the timescales over which recharge takes place may also drive changes in the natural composition of dissolved organic carbon in these groundwaters. Such changes have the potential to influence both the spatial and temporal evolution of the current groundwater arsenic hazard in this region

The Sec1p/Munc18 (SM) protein, Vps45p, cycles on and off membranes during vesicle transport

Protein phosphatase 1 (PP1, Glc7p) functions in the final stage of SNARE-mediated vesicle transport between docking and fusion. During this process, trans-SNARE complexes, formed between molecules in opposing membranes, convert to cis-complexes, with all participants in the same lipid bilayer. Here, we show that glc7 mutant cells accumulate SNARE complexes. These complexes are clearly different from those found in either wild-type or sec18–1 cells as the Sec1p/Munc18 (SM) protein Vps45p does not bind to them. Given that PP1 controls fusion, the SNARE complexes that accumulate in glc7 mutants likely represent trans-SNARE complexes. Vps45p dissociates from the membrane in the absence of PP1 activity, but rapidly reassociates after its reactivation. These data reveal that SM proteins cycle on and off membranes in a stage-specific manner during the vesicle transport reaction, and suggest that protein phosphorylation plays a key role in the regulation of this cycle

Software Tools for Developing and Simulating the NASA LaRC CMF Motion Base

The NASA Langley Research Center (LaRC) Cockpit Motion Facility (CMF) motion base has provided many design and analysis challenges. In the process of addressing these challenges, a comprehensive suite of software tools was developed. The software tools development began with a detailed MATLAB/Simulink model of the motion base which was used primarily for safety loads prediction, design of the closed loop compensator and development of the motion base safety systems1. A Simulink model of the digital control law, from which a portion of the embedded code is directly generated, was later added to this model to form a closed loop system model. Concurrently, software that runs on a PC was created to display and record motion base parameters. It includes a user interface for controlling time history displays, strip chart displays, data storage, and initializing of function generators used during motion base testing. Finally, a software tool was developed for kinematic analysis and prediction of mechanical clearances for the motion system. These tools work together in an integrated package to support normal operations of the motion base, simulate the end to end operation of the motion base system providing facilities for software-in-the-loop testing, mechanical geometry and sensor data visualizations, and function generator setup and evaluation

Novel single nucleotide polymorphism-based assay for genotyping Mycobacterium avium subsp. paratuberculosis

Typing of Mycobacterium avium subspecies paratuberculosis strains presents a challenge, since they are genetically monomorphic and traditional molecular techniques have limited discriminatory power. The recent advances and availability of whole-genome sequencing have extended possibilities for the characterization of Mycobacterium avium subspecies paratuberculosis, and whole-genome sequencing can provide a phylogenetic context to facilitate global epidemiology studies. In this study, we developed a single nucleotide polymorphism (SNP) assay based on PCR and restriction enzyme digestion or sequencing of the amplified product. The SNP analysis was performed using genome sequence data from 133 Mycobacterium avium subspecies paratuberculosis isolates with different genotypes from 8 different host species and 17 distinct geographic regions around the world. A total of 28,402 SNPs were identified among all of the isolates. The minimum number of SNPs required to distinguish between all of the 133 genomes was 93 and between only the type C isolates was 41. To reduce the number of SNPs and PCRs required, we adopted an approach based on sequential detection of SNPs and a decision tree. By the analysis of 14 SNPs Mycobacterium avium subspecies paratuberculosis isolates can be characterized within 14 phylogenetic groups with a higher discriminatory power than mycobacterial interspersed repetitive unit–variable number tandem repeat assay and other typing methods. Continuous updating of genome sequences is needed in order to better characterize new phylogenetic groups and SNP profiles. The novel SNP assay is a discriminative, simple, reproducible method and requires only basic laboratory equipment for the large-scale global typing of Mycobacterium avium subspecies paratuberculosis isolates

Species delimitation and phylogeny of a New Zealand plant species radiation

<p>Abstract</p> <p>Background</p> <p>Delimiting species boundaries and reconstructing the evolutionary relationships of late Tertiary and Quaternary species radiations is difficult. One recent approach emphasizes the use of genome-wide molecular markers, such as amplified fragment length polymorphisms (AFLPs) and single nucleotide polymorphisms (SNPs), to identify distinct metapopulation lineages as taxonomic species. Here we investigate the properties of AFLP data, and the usefulness of tree-based and non-tree-based clustering methods to delimit species and reconstruct evolutionary relationships among high-elevation <it>Ourisia </it>species (Plantaginaceae) in the New Zealand archipelago.</p> <p>Results</p> <p>New Zealand <it>Ourisia </it>are shown to comprise a geologically recent species radiation based on molecular dating analyses of ITS sequences (0.4–1.3 MY). Supernetwork analyses indicate that separate tree-based clustering analyses of four independent AFLP primer combinations and 193 individuals of <it>Ourisia </it>produced similar trees. When combined and analysed using tree building methods, 15 distinct metapopulations could be identified. These clusters corresponded very closely to species and subspecies identified on the basis of diagnostic morphological characters. In contrast, Structure and PCO-MC analyses of the same data identified a maximum of 12 and 8 metapopulations, respectively. All approaches resolved a large-leaved group and a small-leaved group, as well as a lineage of three alpine species within the small-leaved group. We were unable to further resolve relationships within these groups as corrected and uncorrected distances derived from AFLP profiles had limited tree-like properties.</p> <p>Conclusion</p> <p><it>Ourisia </it>radiated into a range of alpine and subalpine habitats in New Zealand during the Pleistocene, resulting in 13 morphologically and ecologically distinct species, including one reinstated from subspecies rank. Analyses of AFLP identified distinct metapopulations consistent with morphological characters allowing species boundaries to be delimited in <it>Ourisia</it>. Importantly, Structure analyses suggest some degree of admixture with most species, which may also explain why the AFLP data do not exhibit sufficient tree-like properties necessary for reconstructing some species relationships. We discuss this feature and highlight the importance of improving models for phylogenetic analyses of species radiations using AFLP and SNP data.</p

Process Optimisation of Steam Explosion Parameters on Multiple Lignocellulosic Biomass using Taguchi Method:A Critical Appraisal

Xylitol is a low calorie sweetener that can be produced through a bioconversion approach from lignocellulosic biomass that requires pretreatment prior to the bioconversion of xylose to xylitol. Steam explosion (SE) is an industrially scalable pretreatment (PT) process with the potential to liberate xylose monomers, however SE-PT has not been optimised for xylose release from multiple feedstock. The effect of pressure, substrate weight, phosphoric acid loading concentration and residence time on four feedstock (wheat straw (WS), corn stover (CS), Miscanthus (M), and willow (W)) for xylose release and minimal fermentation inhibitor productions (furfural and 5-hydroxymethylfurfural (HMF)) was investigated using the Taguchi methodology for design of experiment (DoE) with variation at four levels (44). An L16 orthogonal array design was utilised and all factors indicated influence on xylose release and inhibitor formation and the resulting xylose rich hydrolysate assessed for bioconversion to xylitol.. The L16 DoE gave hydrolysates containing 75-95% of xylose content in the original biomass, whilst retaining cellulose and lignin components in the fibre. The level of inhibitors were within boundary limits to enable microbial fermentation of the hydrolysates to xylitol. Fine tuning of the overall evaluation criteria (OEC) model imbibing 1.5 kg feedstock in 1.2% w/v orthophosphoric acid, 12 bar(g) and 6 minutes residence time resulted in 90% xylose recovery and production of >1000 L of wheat straw hydrolysate for bioconversion to xylitol. The advantages and limitations of the Taguchi OEC model and further improvements to this process are discussed in a biorefining contextpublishersversionPeer reviewe

Temporal and Spatial Trends of Northern Bobwhite Survival and Nest Success

The northern bobwhite (Colinus virginianus) has been declining in abundance across North America for many years. It is unknown, however, if other population variables also exhibit this downward trajectory. We conducted a retrospective-analysis of annual survival and nest success based on a literature review of 64 studies and compared these estimates temporally and spatially. We hypothesized that increased management efforts influenced bobwhite survival in the 1990s. Evidence from linear splining indicated survival trends changed in 1994. Thus, we compared trends across 3 periods: before 1994, after 1994, and overall. Mean (6 SD) annual survival was 13.9 6 9.4% across 31 studies from 1970 to 2007. Annual survival decreased 0.534% per year during 1970–1994 and stabilized thereafter. This stabilization in survival occurred along latitudinal and longitudinal gradients in which survival decreased at the northern and western periphery of the bobwhite range. Our linear splining models did not support the hypothesis that trends in nest success changed in the 1990s; thus, we only compared trends across the overall, 1924–2008 range of studies. Mean nest success across 33 studies was 44.4 6 15.2% during this interval and increased slightly across the 1924–2008 range of studies. We observed latitudinal gradients in nest success. Nest success was lowest at the northern periphery of the bobwhite range; it decreased 0.90% per degree of latitude. Annual survival stabilized after 1994 despite monotonic declines in bobwhite abundance since at least the 1960s. Range-wide survival and nest success trends may not parallel trends in abundance, particularly after 1990, which suggests biologists may not fully understand the range-wide population ecology of bobwhites. This lends support for the need to monitor other aspects of the bobwhites range-wide population dynamics as supplements to range-wide abundance

Here Today, Gone Tomorrow: Understanding Freshman Attrition Using Person-Environment Fit Theory

Person-Environment (PE) fit theory was used to explore the relationship between student involvement and freshman retention. Incoming freshmen (N=382) were followed longitudinally in a twowave panel study, the summer before beginning college, and again during the spring of their freshman year. Involvement levels, a variety of summer and spring preferences (Ps), and spring perceptions (Es) regarding specific aspects of their college environment were assessed. Twelve PE fit indicators were derived and compared with respect to their relationship with student involvement and retention. Results indicated that involvement was linked to some PE fit indicators. Traditional parametric statistical analyses were compared with a new, nonparametric technique, Classification Tree Analysis (CTA), to identify the most accurate classification model for use in designing potential attrition interventions. Discriminant analysis was 14% more accurate than CTA in classifying returners (97% vs. 85%), but CTA was 962% more accurate classifying dropouts (8% vs. 84%). CTA identified nine clusters— five of returners and four of dropouts, revealing that different subgroups of freshmen chose to return (and stay) for different reasons. Students’ end-of-the-year preferences appear to be more important than anticipated preferences, college perceptions, or PE fit level